\relax 
\bibstyle{biophysj}
\providecommand {\FN@pp@footnotehinttrue }{}
\providecommand {\FN@pp@footnote@aux }[2]{}
\@input{acknowledgement.aux}
\FN@pp@footnotehinttrue 
\FN@pp@footnotehinttrue 
\FN@pp@footnotehinttrue 
\FN@pp@footnotehinttrue 
\FN@pp@footnotehinttrue 
\@input{introduction.aux}
\FN@pp@footnotehinttrue 
\@writefile{toc}{\contentsline {part}{I\hspace  {1em}Running Brahms}{3}}
\@input{input/inputParameters.aux}
\FN@pp@footnotehinttrue 
\@input{runningSimulations/run.aux}
\FN@pp@footnotehinttrue 
\@input{output/out.aux}
\FN@pp@footnotehinttrue 
\@input{visualization/vis.aux}
\FN@pp@footnotehinttrue 
\@input{analysis/an.aux}
\FN@pp@footnotehinttrue 
\@input{bench/benchmarks.aux}
\FN@pp@footnotehinttrue 
\FN@pp@footnotehinttrue 
\@writefile{toc}{\contentsline {part}{II\hspace  {1em}Background}{21}}
\@input{md/md.aux}
\FN@pp@footnotehinttrue 
\@input{biophys/biophys.aux}
\FN@pp@footnotehinttrue 
\bibdata{/home/orsi/biblio.bib}
\bibcite{orsi11elba}{{1}{2011}{{Orsi and Essex}}{{}}}
\bibcite{rapa}{{2}{2004}{{Rapaport}}{{}}}
\bibcite{dullw97a}{{3}{1997}{{Dullweber et~al.}}{{Dullweber, Leimkuhler, and McLachlan}}}
\bibcite{mario08}{{4}{2008}{{Orsi et~al.}}{{Orsi, Haubertin, Sanderson, and Essex}}}
\bibcite{marioSmall}{{5}{2009}{{Orsi et~al.}}{{Orsi, Sanderson, and Essex}}}
\bibcite{marioDmpcDopc}{{6}{2010}{{Orsi et~al.}}{{Orsi, Michel, and Essex}}}
\bibcite{marioDH}{{7}{2010}{{Orsi and Essex}}{{}}}
\bibcite{marioTriclos}{{8}{2011}{{Orsi et~al.}}{{Orsi, Noro, and Essex}}}
\bibcite{gmx31}{{9}{2001}{{van~der Spoel et~al.}}{{van~der Spoel, van Buuren, Apol, Meulen\discretionary {-}{}{}hoff, Tieleman, Sij\discretionary {-}{}{}bers, Hess, Feenstra, Lindahl, van Drunen, and Berendsen}}}
\bibcite{mouritsen}{{10}{2005}{{Mouritsen}}{{}}}
\bibcite{winger09}{{11}{2009}{{Winger et~al.}}{{Winger, Trzesniak, Baron, and van Gunsteren}}}
\bibcite{HUMP96}{{12}{1996}{{Humphrey et~al.}}{{Humphrey, Dalke, and Schulten}}}
\bibcite{ber84}{{13}{1984}{{Berendsen et~al.}}{{Berendsen, Postma, van Gunsteren, Di~Nola, and Haak}}}
\bibcite{morishita00}{{14}{2000}{{Morishita}}{{}}}
\bibcite{harve98a}{{15}{1998}{{Harvey et~al.}}{{Harvey, Tan, and Cheatham~III}}}
\bibcite{patra04a}{{16}{2004}{{Patra et~al.}}{{Patra, Karttunen, Hyvonen, Falck, and Vattulainen}}}
\bibcite{klauda06b}{{17}{2006}{{Klauda et~al.}}{{Klauda, Brooks, and Pastor}}}
\bibcite{roark09}{{18}{2009}{{Roark and Feller}}{{}}}
\bibcite{allen}{{19}{1987}{{Allen and Tildesley}}{{}}}
\bibcite{leach}{{20}{2001}{{Leach}}{{}}}
\bibcite{frenkel}{{21}{2002}{{Frenkel and Smit}}{{}}}
\bibcite{schlick}{{22}{2002}{{Schlick}}{{}}}
\bibcite{luck90}{{23}{1990}{{Luckhurst et~al.}}{{Luckhurst, Stephens, and Phippen}}}
\bibcite{leimkuhler}{{24}{2004}{{Leimkuhler and Reich}}{{}}}
\bibcite{tuckerman00}{{25}{2000}{{Tuckerman and Martyna}}{{}}}
\bibcite{mclac93a}{{26}{1993}{{McLachlan}}{{}}}
\bibcite{grays94a}{{27}{1994}{{Gray et~al.}}{{Gray, Noid, and Sumpter}}}
\bibcite{mille02a}{{28}{2002}{{Miller~III et~al.}}{{Miller~III, Eleftheriou, Pattnaik, Ndirango, Newns, and Martyna}}}
\bibcite{omely02b}{{29}{2002}{{Omelyan et~al.}}{{Omelyan, Mryglod, and Folk}}}
\bibcite{prapr05a}{{30}{2005}{{Praprotnik and Janezic}}{{}}}
\bibcite{allen04}{{31}{2004}{{Allen}}{{}}}
\FN@pp@footnotehinttrue 
\bibcite{knuth68}{{32}{1968}{{Knuth}}{{}}}
\bibcite{verlet67}{{33}{1967}{{Verlet}}{{}}}
\bibcite{thompson09}{{34}{2009}{{Thompson et~al.}}{{Thompson, Plimpton, and Mattson}}}
\bibcite{alejandre95}{{35}{1995}{{Alejandre et~al.}}{{Alejandre, Tildesley, and Chapela}}}
\bibcite{cheng96}{{36}{1996}{{Cheng and Merz}}{{}}}
\bibcite{brown95}{{37}{1995}{{Brown and Neyertz}}{{}}}
\bibcite{carpenter02}{{38}{2002}{{Carpenter}}{{}}}
\bibcite{gulli04}{{39}{2004}{{Gullingsrud and Schulten}}{{}}}
\bibcite{veld03}{{40}{2003}{{in~`t Veld and Rutledge}}{{}}}
\bibcite{procacci97}{{41}{1997}{{Procacci et~al.}}{{Procacci, Darden, Paci, and Marchi}}}
\bibcite{refson}{{42}{2001}{{Refson}}{{}}}
\bibcite{bussi09}{{43}{2009}{{Bussi et~al.}}{{Bussi, Zykova-Timan, and Parrinello}}}
\bibcite{voet}{{44}{2004}{{Voet and Voet}}{{}}}
\bibcite{simmons}{{45}{}{{sim}}{{}}}
\bibcite{dowhan}{{46}{2004}{{Dowhan and Bogdanov}}{{}}}
\bibcite{berg}{{47}{2002}{{Berg et~al.}}{{Berg, Tymoczko, and Stryer}}}
\bibcite{simons00}{{48}{2000}{{Simons and Toomre}}{{}}}
\bibcite{ualr}{{49}{}{{ual}}{{}}}
\bibcite{scq}{{50}{}{{scq}}{{}}}
\bibcite{steve}{{51}{}{{ste}}{{}}}
\bibcite{southall02}{{52}{2002}{{Southall et~al.}}{{Southall, Dill, and Haymet}}}
\bibcite{chandler05}{{53}{2005}{{Chandler}}{{}}}
\bibcite{hamley}{{54}{2007}{{Hamley}}{{}}}
\bibcite{nagle00a}{{55}{2000}{{Nagle and Tristram-{N}agle}}{{}}}
\bibcite{koeni97a}{{56}{1997}{{Koenig et~al.}}{{Koenig, Strey, and Gawrisch}}}
\bibcite{feller-dppc}{{57}{}{{fel}}{{}}}
\bibcite{akuts91a}{{58}{1991}{{Akutsu and Nagamori}}{{}}}
\bibcite{jseelig74}{{59}{1974}{{Seelig and Niederberger}}{{}}}
\bibcite{cevc}{{60}{1987}{{Cevc and Marsh}}{{}}}
\bibcite{janiak79}{{61}{1979}{{Janiak et~al.}}{{Janiak, Small, and Shipley}}}
\bibcite{templer98}{{62}{1998}{{Templer et~al.}}{{Templer, Castle, Curran, Rumbles, and Klug}}}
\bibcite{sedd95}{{63}{1995}{{Seddon and Templer}}{{}}}
\bibcite{yang03}{{64}{2003}{{Yang et~al.}}{{Yang, Ding, and Huang}}}
\bibcite{kozlovsky04}{{65}{2004}{{Kozlovsky et~al.}}{{Kozlovsky, Efrat, Siegel, and Kozlov}}}
\bibcite{siegel04}{{66}{2004}{{Siegel and Kozlov}}{{}}}
\bibcite{shearman06}{{67}{2006}{{Shearman et~al.}}{{Shearman, Ces, Templer, and Seddon}}}
\bibcite{kamo06}{{68}{2006}{{Kamo et~al.}}{{Kamo, Nakano, Kuroda, and Handa}}}
\bibcite{curnow04}{{69}{2004}{{Curnow et~al.}}{{Curnow, Lorch, Charalambous, and Booth}}}
\bibcite{mohr05}{{70}{2005}{{Mohr et~al.}}{{Mohr, Gribble, Lin, Eckenhoff, and Cantor}}}
\bibcite{curran99}{{71}{1999}{{Curran et~al.}}{{Curran, Templer, and Booth}}}
\bibcite{meijberg02}{{72}{2002}{{Meijberg and Booth}}{{}}}
\bibcite{brink04}{{73}{2004}{{van den Brink-van~der Laan et~al.}}{{van den Brink-van~der Laan, Killian, and de~Kruijff}}}
\bibcite{hong04}{{74}{2004}{{Hong and Tamm}}{{}}}
\bibcite{bowie05}{{75}{2005}{{Bowie}}{{}}}
\bibcite{attard00}{{76}{2000}{{Attard et~al.}}{{Attard, Templer, Smith, Hunt, and Jackowski}}}
\bibcite{davies01}{{77}{2001}{{Davies et~al.}}{{Davies, Epand, Kraayenhof, and Cornell}}}
\bibcite{fanani04}{{78}{2004}{{Fanani et~al.}}{{Fanani, Topham, Walsh, and Epand}}}
\bibcite{sen91}{{79}{1991}{{Sen et~al.}}{{Sen, Isac, and Hui}}}
\bibcite{ruiz98}{{80}{1998}{{Ruiz-{A}rguello et~al.}}{{Ruiz-{A}rguello, Goni, and Alonso}}}
\bibcite{botelho02}{{81}{2002}{{Botelho et~al.}}{{Botelho, Gibson, Thurmond, Wang, and Brown}}}
\bibcite{wang02}{{82}{2002}{{Wang et~al.}}{{Wang, Botelho, Martinez, and Brown}}}
\bibcite{botelho06}{{83}{2006}{{Botelho et~al.}}{{Botelho, Huber, Sakmar, and Brown}}}
\bibcite{keller93}{{84}{1993}{{Keller et~al.}}{{Keller, Bezrukov, Gruner, Tate, Vodyanoy, and Parsegian}}}
\bibcite{perozo02}{{85}{2002}{{Perozo et~al.}}{{Perozo, Kloda, Cortes, and Martinac}}}
\bibcite{jensen04}{{86}{2004}{{Jensen et~al.}}{{Jensen, Mouritsen, and Peters}}}
\bibcite{rosto06}{{87}{2006}{{Rostovtseva et~al.}}{{Rostovtseva, Kazemi, Weinrich, and Bezrukov}}}
\bibcite{helfrich73}{{88}{1973}{{Helfrich}}{{}}}
\bibcite{marsh06}{{89}{2006}{{Marsh}}{{}}}
\bibcite{shinoda98}{{90}{1998}{{Shinoda et~al.}}{{Shinoda, Shimizu, and Okazaki}}}
\bibcite{clarke97}{{91}{1997}{{Clarke}}{{}}}
\bibcite{clarke01}{{92}{2001}{{Clarke}}{{}}}
\bibcite{cladera01}{{93}{2001}{{Cladera et~al.}}{{Cladera, Martin, and O'{S}hea}}}
\bibcite{cladera99}{{94}{1999}{{Cladera et~al.}}{{Cladera, Martin, Ruysschaert, and O'{S}hea}}}
\bibcite{franklin93}{{95}{1993}{{Franklin and Cafiso}}{{}}}
\bibcite{starke05}{{96}{2005}{{Starke-{P}eterkovic et~al.}}{{Starke-{P}eterkovic, Turner, Else, and Clarke}}}
\bibcite{rokitskaya02}{{97}{2002}{{Rokitskaya et~al.}}{{Rokitskaya, Kotova, and Antonenko}}}
\bibcite{maggio99}{{98}{1999}{{Maggio}}{{}}}
\bibcite{cladera98}{{99}{1998}{{Cladera and O'{S}hea}}{{}}}
\bibcite{gelbart00}{{100}{2000}{{{Gelbart} et~al.}}{{{Gelbart}, {Bruinsma}, {Pincus}, and {Parsegian}}}}
\bibcite{alakoskela01}{{101}{2001}{{Alakoskela and Kinnunen}}{{}}}
\bibcite{cladera03}{{102}{2003}{{Cladera et~al.}}{{Cladera, O'{S}hea, Hadgraft, and Valenta}}}
\bibcite{cafiso98}{{103}{1998}{{Cafiso}}{{}}}
\bibcite{qin95}{{104}{1995}{{Qin et~al.}}{{Qin, Szabo, and Cafiso}}}
\bibcite{alakoskela04}{{105}{2004}{{Alakoskela et~al.}}{{Alakoskela, Soderlund, Holopainen, and Kinnunen}}}
\bibcite{asawakarn01}{{106}{2001}{{Asawakarn et~al.}}{{Asawakarn, Cladera, and O'{S}hea}}}
\bibcite{oshea03}{{107}{2003}{{O'{S}hea}}{{}}}
\bibcite{luker01}{{108}{2001}{{Luker et~al.}}{{Luker, Flagg, Sha, Luker, Pica, Nichols, and Piwnica-{W}orms}}}
\bibcite{gawrisch92}{{109}{1992}{{Gawrisch et~al.}}{{Gawrisch, Ruston, Zimmerberg, Parsegian, Rand, and Fuller}}}
\bibcite{schamberger02}{{110}{2002}{{Schamberger and Clarke}}{{}}}
\bibcite{lairion04}{{111}{2004}{{Lairion and Disalvo}}{{}}}
\bibcite{wang06}{{112}{2006}{{Wang et~al.}}{{Wang, Bose, and Sigworth}}}
\bibcite{sonnleitner99}{{113}{1999}{{Sonnleitner et~al.}}{{Sonnleitner, Schutz, and Schmidt}}}
\bibcite{tabony91}{{114}{1991}{{Tabony and Perly}}{{}}}
\bibcite{filip03b}{{115}{2003}{{Filippov et~al.}}{{Filippov, Or{\"a}dd, and Lindblom}}}
\bibcite{almeida92}{{116}{1992}{{Almeida et~al.}}{{Almeida, Vaz, and Thompson}}}
\bibcite{vaz91}{{117}{1991}{{Vaz and Almeida}}{{}}}
\bibcite{cohen59}{{118}{1959}{{Cohen and Turnbull}}{{}}}
\bibcite{turnbull61}{{119}{1961}{{Turnbull and Cohen}}{{}}}
\bibcite{turnbull70}{{120}{1970}{{Turnbull and Cohen}}{{}}}
\bibcite{oleary87}{{121}{1987}{{O'{L}eary}}{{}}}
\FN@pp@footnotehinttrue 
